Exam 3

in 1953 these scientists determined the structure of DNA which revealed how DNA might replicated and encode info for proteins

False, while common in bacteria, they are rare in eukaryotes

T/F: operons are common in both eukaryotes and bacteria

1) to keep the lifetime short of certain proteins

2) to remove those that are damaged or misfolded

why would protease need to destroy a protein?

protease

enzymes that degrade proteins first to short peptides and then to individual amino acids

3' end

what end can you add nucleotides on for DNA replication, the 5' end or 3' end of the parent chain?

it would be harder to break DNA with C-G pairings because C-G has 3 H-bonds whereas A-T only has 2

would it be harder to break DNA with a lot of C-G pairings or DNA with a lot of A-T pairings?

chromosomes

discovered as threadlike structures in the nucleus of eukaryotic cells that become visible as the cells begin to divide

That DNA replication is semi-conservative

what did the Meselson-Stahl experiment prove?

1. The small ribosomal subunit along with the translation initiation factors (including initiator tRNA) bind to mRNA

2. The small ribosomal subunit, initiator tRNA, and initiation factors move along mRNA, searching for AUG

3. Once AUG is found the initiation factors go while the large ribosomal subunit comes in, putting initiation tRNA in the P site

4. The next tRNA binds in the A site

5. A peptide bond forms

Explain the 5 steps of translation initiation.

The gene would not be expressed- the fly would exhibit white eyes. Transcription machinery cannot access highly condensed regions of DNA  white eye in flies IMPORTANT: drosophila genes are named after their mutant forms. The wild-type (normal) form of the gene expresses red eyes. If the gene is mutated (not expressed), then we observe the mutant phenotype for which it is named (white eyes)

What would happen if the white-eye gene in drosophila accidentally becomes packaged into heterochromatin?

Euchromatin

the rest of the interphase chromatin, chromatin that is more decondensed

chromosomes

contains both proteins and DNA

deoxyribonucleic acid

consists of 2 long polynucleotide chains/strands, each of which is composed of 4 nucleotide subunits and held together via Hydrogen bonds

Because DNA is chemically simple while proteins are diverse

Why did people used to think that proteins made genes?

Fred Griffith

which scientist showed that heat-killed, infectious bacteria can transform harmless, living bacteria into pathogenic ones

Name the scientists who prepared an extract from the S strain of pneumonia and showed that DNA is the "transforming principle" that would change harmless R strands into killer S strands.

Avery, MacLeod, and McCarty experiment of fractionation

The first evidence that DNA could serve as the genetic material, not protein

T2 viruses are made entirely of DNA and Protein. DNA was labeled with 32P while protein was labeled with 35S. The viruses were allowed to infect and replicate in E. coli cells. Blending the cells and separation of the bacteria from the empty viral heads showed that 32P labeled DNA was still in bacteria.

describe Alfred Hershey and Martha Chase's experiment

sugar + phosphate + base

What is a nucleotide?

DNA double helix

held together via hydrogen-bonding between the bases on different strands

Base Pairs

each purine-pyrimidine pair; this enables them to be packed in the energetically most favorable arrangement in the helix's interior

phosphodiester bonds

nucleotides are linked together COVALENTLY by (blank) bonds through the 3' OH group of one sugar and the 5' phosphate group of its neighbor,

The directional linkage; the sugars 3' OH end vs the sugars 5' phosphate end

what gives each polynucleotide stand a chemical polarity?

they are oriented with opposite polarities

each base pair can fit together within the double helix bc the 2 strands run antiparallel to each other meaning....

It refers to the fact that A pairs with T and G pairs with C

What does the phrase 'DNA is complementary' refer to?

The genetic code

the correspondence between the 4-letter nucleotide alphabet of DNA and the 20-letter amino acid alphabet of proteins

Gene expression

the process by which the nucleotide sequence of a gene is transcribed into the nucleotide sequence of an RNA molecule which is then translated into the amino acid sequence of a protein

euk: chromosomes

prok: circular

Eukaryotic DNA is packed into blank while bacteria DNA is packaged blank

chromatin

the complex of DNA and protein

the sex chromosomes in males where a Y comes from dad and X comes from mom

the only nonhomologous chromosome pairs are...

karyotype

an ordered display of the full set of 46 human chromosomes

Gene

a segment of DNA that contains the instructions for making a particular protein or RNA molecule

True

T/F: usually, the more complex the organism, the larger its genome

True

T/F: two closely related species can have similar genome sizes but very different chromosome numbers

interphase

phase where the chromosomes are extended as long, thin, tangled threads of DNA in the nucleus and cannot be easily distinguished in the light microscope

replication origin

eukaryotic chromosomes contain many of these; sequence where replication begins

Telomeres

formed at each end of a chromosome; these contain repeated nucleotide sequences that are required for the ends of chromosomes to be replicated and cap the ends of DNA, preventing them from being mistaken by cells as broken DNA

1) a centromere

2) two telomeres

3) several origins of replication

What are the 3 DNA sequence elements needed to produce a eukaryotic chromosome that can be replicated

M phase

phase where the centromere attaches the duplicated chromosomes to the mitotic spindle so that 1 copy is distributed to each daughter cell when it divides

true

T/F: interphase chromosomes are not randomly distributed within the nucleus

chromosomes

DNA molecules with their associated proteins are called chromatids; once the sister chromatids separate, they are considered...

nuclear lamina

the protein meshwork that supports the nuclear envelope

nucleolus

where the parts of the different chromosomes carrying genes that encode ribosomal RNA cluster together; rRNA is made here and combine with proteins to become ribosomes

nucleolus

the most prominent structure in the interphase nucleus;

true

T/F: each interphase chromosome is seen to occupy its own discrete territory within the nucleus

nucleosomes

the basic units of eukaryotic chromosome structure

Histones and nonhistones

proteins that bind to DNA to form eukaryotic chromosomes are divided into what two general classes?

False

T/F: DNA in mitotic chromosomes is less compact than in interphase chromosomes

nucleases

structure of nucleosome core particles were determined after isolating nucleosomes by treating unfolded chromatin with these enzymes

nucleases

break down DNA by cutting the phosphodiester bonds between nucleotides

a mutation in this kind of cell will be passed on to all the cells in the body , including the cells responsible for production of the next generation

RNA splicing

a process in eukaryotic cells in which segments of an RNA transcript are removed

genes

the segments of DNA that are transcribed into RNA are called...

True

T/F: a cell can express different genes in different rates

transcription

1st step of gene expression; a DNA nucleotide is copied in the form of RNA nucleotide

1) nucleotides are ribonucleotides

2) it has U instead of T

3) it is single stranded so it can fold into many shapes

how does RNA differ from DNA?

RNA

these molecules can form intramolecular base pairs and fold into specific structures

transcription

process that produces RNA that's complementary to one strand of DNA

RNA polymerase

enzyme that links the incoming ribonucleotide covalently to the growing RNA chain

RNA transcript

the RNA chain produced by transcription; is elongated 1 nucleotide at a time and has a nucleotide sequence exactly complementary to the strand of DNA used as the template

true

T/F: RNA molecules are much shorter than DNA molecules bc RNA is copied from only a limited region of DNA

RNA polymerase

DNA is transcribed into RNA with what enzyme?

RNA polymerase

catalyzes the formation of the phosphodiester bonds that link nucleotides together and form the sugar-phosphate backbone of the RNA chain

RNA polymerase can create and RNA chain without a primer

what is a major difference between RNA polymerase and DNA polymerase?

true

T/F: cells produce various types of RNA

3' to 5' direction

what direction does RNA polymerase move along the DNA template

messenger RNA

code for proteins; the RNA molecules encoded by genes which ultimately direct the synthesis of proteins; these carry info transcribed from 1 gene so they code for a single protein in euks and for several proteins in proks

ribosomal RNA

forms the structural and catalytic core of the ribosomes; catalyze protein synthesis

transfer RNA

act as adaptors that select specific amino acids and hold them in place on ribosome for their incorporation into protein; serve as adaptors between mRNA and amino acids during protein synthesis

micro RNA

serve as key regulators of eukaryotic gene expression

gene expression

the process by which the info encoded in a DNA sequence is translated into a product that has some effect on a cell or organism

promoter

gene region which contains a specific sequence of nucleotides that lies immediately upstream of the starting point for RNA synthesis; RNA polymerase latches on tightly only after it has encountered this region

terminator aka stop site

chain elongation continues until the enzyme encounters this signal where the polymerase halts and releases both DNA template and newly made RNA transcript; this is contained within the gene and is transcribed into the 3' end of the new RNA

sigma factor

in bacteria this is a subunit of RNA polymerase that recognizes the promoter sequence in DNA without having to separate the DNA strands

the promotor's polarity; it uses the DNA strand oriented in the 3'-5' direction as template so that it can synthesize in the 5'-3' direction

How does RNA polymerase know which strand of DNA to use as the template?

general transcription factors

these are a part of a large set of accessory proteins which must assemble at each promoter along with RNA polymerase before it begins transcription

true

T/F: one an individual chromosome, some genes are transcribed using 1 DNA strand as a template and others are transcribed from the other DNA strand

1) bacteria contain a single RNA polymerase while euks have 3

2) bacteria can initiate transcription on its own while euk requires help from accessory proteins

how is transcription initiation in eukaryotes different than bacteria?

RNA polymerase I

type of polymerase that transcribes most rRNA genes

RNA polymerase II

type of polymerase that transcribes all protein coding genes, miRNA genes, and genes for other noncoding RNA's like those in splicosomes

RNA polymerase III

type of polymerase that transcribes tRNA genes, 55 rRNA gene, and genes for many other small RNAs

general transcription factors

eukaryotic RNA polymerase requires...

General Transcription Factors

accessory proteins assemble on the promoter where they position the RNA polymerase and pull apart the DNA double helix to expose the template strand, allowing the polymerase to begin transcription;

TATA box

many promoters contain this DNA sequence; this is recognized by a subunit of the general transcript factor

TATA-hinding protein

binds to the TATA box and bends the DNA double helix

complete transcription initiation

once TFIID has been bound to the TATA box, the other factors assemble, along with RNA polymerase II, to form a...

nucleus

eukaryotic mRNAs ate processed in the...

Bacterial cells

cells where its DNA lies directly exposed to the cytoplasm which contains the ribosomes on which protein synthesis takes place; as an mRNA molecule starts to be synthesized, ribosomes immediately attach to the free 5' end of the RNA transcript and begin translating it into protein

eukaryotic cells

cells where DNA is enclosed within the nucleus so transcription takes place in the nucleus but protein synthesis takes place on ribosomes in the cytoplasm;

capping

splicing

polyadenylation

Name the RNA processing steps that occur as RNA is being synthesized and before mRNA is transported out of the nucleus through small pores in the nuclear envelope

RNA polymerase II

the enzymes responsible for RNA processing ride on the phosphorylated talk of eukaryotic (BLANK) as it synthesizes an RNA molecule and they process the transcript as it emerges from this

1)RNA capping

2)Polyadenylation

what are the 2 processing steps that occur on RNA transcripts destined to become mRNA molecules?

RNA capping

modifies the 5' end of the RNA transcript by the addition of an atypical nucleotide (G) after RNA polymerase II has barely produced a whole gene

Polyadenylation

provides a newly transcribed mRNA with a special structure at its 3' end which is 1st trimmed by an enzyme then a 2nd enzyme adds A nucleotides to the end (poly-A-tail)

RNA capping and polyadenylation

modification processes that increase the stability of a eukaryotic mRNA molecule, facilitate its export from the nucleus to the cytoplasm and mark the RNA as mRNA; they make sure both ends of the mRNA are present before protein synthesis begins

Phosphorylation

what occurs on the tail of RNA polymerase II that allows RNA-processing proteins to assemble there?

introns

noncoding sequences that interrupt protein coding genes in eukaryotes

Introns

removed from pre-mRNA by RNA splicing

No

Do bacterial genes contain introns?

process where introns are removed from a newly synthesized RNA and the exons are stitched together

True

T/F: RNA splicing is carried out largely by RNA molecules rather than proteins

small nuclear RNAs (snRNAs)

RNA molecules that carry out splicing are packaged with additional proteins to form these; they recognize splice-site sequences through complementary base pairing between RNA and pre-mRNA;

spliceosome

snRNPs form the core of these; the large assembly of RNA and protein molecules that carry out RNA splicing in the nucleus

alternative splicing

refers to how the transcripts of many eukaryotic genes can be spliced in different ways, each of which producing a different protein; this increases the genome coding potential

intron

special nucleotide sequences in pre-mRNA transcript signal the beginning and end of an...

the 5' end is made by the initiation of transcription by one RNA polymerase, the 3' end is made by the termination; there's no nucleus so both transcription and translation take place in a common compartment.

the nucleotide sequence of an mRNA is translated into the amino acid sequence of a protein via...

sets of 3 nucleotides

mRNA sequence is decoded in sets of how many nucleotides

Translation

the conversion of the information in RNA into protein

Genetic Code

the rules by which the nucleotide sequence of a gene, through an intermediary mRNA molecule, is translated into the amino acid sequence of a protein

64

how many possible combinations of 3 nucleotides (codon) are possible?

codon

a group of consecutive nucleotides in RNA; each of these specifies 1 amino acid

Reading Frames

one of the 3 possible ways in which a set of successive nucleotide triplets can be translated into protein, depending on which nucleotide serves as the starting point

True, this is talking about the 3 reading frames

t/F: the same mRNA sequence can specify 3 completely different amino acid sequences depending on where translation begins

tRNA

what kind of RNA molecules match amino acids to codons in mRNA?

transfer RNA

translation of mRNA into protein depends on these adaptor molecules that can recognize and bind to a codon at one site on their surface and bind to an amino acid at another site

anticodon

a set of 3 consecutive nucleotides that bind, through base-pairing, to the complementary codon

True, this is called wobble base-pairing; it explains why so many of the alternative codons for an amino acid differ only in their 3rd nucleotide

T/F: some tRNA's can tolerate a mismatched 3rd nucleotide in a codon

true

T/F: specific enzymes couple tRNAs to the correct amino acid

aminoacyl-tRNA synthetase

recognition and attachment of the correct amino acid to a tRNA molecule depend on these enzymes

aminoacyl-tRNA synthetase

these covalenty couple each amino acid to its appropriate set of tRNA molecules

20, one for each amino acid

How many aminoacyl-tRNA synthetases are there?

aminoacyl-tRNA synthetase and tRNAs

the genetic code is translated by the cooperation of what two adaptors

ribosomes

the mRNA message is decoded by what?

ribosome

a large complex made from dozens of small proteins and several rRNAs

small ribosomal subunit

what matches the tRNAs to the codons of the mRNA

large ribosomal subunit

what catalyzes the formation of the peptide bonds that covalently link the amino acids together into a polypeptide chain

cytoplasm

where are ribosomes located in eukaryotic cells?

ribosomes

this translates mRNA's nucleotide sequence into an amino acid sequence, one codon at a time, using the tRNAs as adaptors

true

T/F: when synthesis of a protein is finished, the two ribosomal subunits separate

ribosome

this is a large complex of 4 rRNA's and more than 80 small proteins

A site

what is the first site in ribosome that an appropriately charged tRNA base pairs with a complementary mRNA codon

P site

what is the second site in ribosome where the amino acid is linked to the peptide chain held by tRNA

E site

what is the 3rd site in ribosome that the spent tRNA moves in when the large ribosomal unit shifts forward; this is where tRNA is ejected

translation

takes place in a 4-step cycle

1) a charged tRNA carrying the next amino acid to be added to the polypeptide chain binds to the covalent A site on the ribosome

2) see figure 7-34

Explain the 4 steps of translation

rRNA

What gives the ribosome its overall shape?

Ribozymes

RNA molecules that possess catalytic activity

initiator tRNA

always carries the amino acid methionine so newly made proteins all have methionine as the 1st amino acid at their N-terminal

translation initiation factors

these along with the initiator tRNA are loaded into the P site of the small ribosomal subunit

1) a charged tRNA carrying the next amino acid binds to the A site by forming base pairs with the mRNA codon

2) the OH end of the polypeptide chain is uncoupled from tRNA at the P site and joined to the free amino group linked to the tRNA at the A site

3) a shift of the large subunit moves the 2 tRNAs into the E and P sites of the large subunit

4) small subunit moves exactly 3 nucleotides along the mRNA molecule, bringing it back to the original position

Explain how translation occurs in the ribosome (4 steps, see Movie 7.9)

peptidyl transferase

the catalytic site in rRNA; a highly structured pocket that precisely orients the elongating polypeptide and the charged tRNA, helping translation to occur

true

T/F: RNA rather than protein molecules served as the 1st catalysts for cells

polycistronic

this word describes protaryotic mRNAs as they encode several different proteins whereas eukaryotic mRNA usually carries info for a single protein

UAA

UAG

UGA

what are the 3 stop codons

these are not recognized by a tRNA and don't specify an amino acid but instead signal to the ribosome to stop translation

release factors

proteins that bind to any stop codon that reaches the A site on the ribosome, causing it to catalyze the addition of a water molecule instead of an amino acid to the peptidyl tRNA

proteins

what are made on polyribosomes?

polyribosomes aka polysomes

large cytoplasmic assemblies made of many ribosomes spaced as close as 80 nucleotides apart along a single mRNA molecule

polyribosomes, many ribosomes work on an mRNA simultaneously

what is a way that translation is sped up?

protein breakdown

this is controlled so that the amount of proteins in a cell is regulated

the process of enzymatically breaking down proteins into their amino acids

what is proteolysis?

proteases

the enzymes that degrade proteins, first to short peptides and finally to individual amino acids

proteasomes

present in both the cytosol and the nucleus, these are large protein machines that cause proteolysis to occur

ubiquitin

proteasomes select the proteins that need to be degraded by looking at which of them have been marked for destruction by the covalent attachment of this certain protein

degradation by a proteasome

proteins marked by ubiquitin are destined for...

covalent modification (phosphorylation), the binding of small-molecule cofactors, or association with other protein subunits

what are some example of post-translational modifications some proteins need in order to be useful to the cell?

False, the final concentration of proteins depends on the rate of each of the many steps required

T/F: protein production in a eukaryotic cell requires relatively few steps

an RNA world

what kind of environment may have existed before modern c ells with DNA and proteins evolved

RNA

Which is thought to have come first, RNA or DNA?

ribozyme

an RNA molecule that possesses catalytic activity

true

T/F: nearly all the cells of a multicellular organism contain the same genome; they only differ by changes in gene expression

True, but they differ in their expressed RNAs and proteins

T/F: a neuron and a liver cell share the same genome

Gene Expression

a complex process by which cells selectively direct the synthesis of the many thousands of proteins and RNAs encoded in their genome

differentiation

process by which a cell undergoes a progressive coordinated change to a more specialized cell type, brought about by large-scale changes in gene expression

True

T/F: cells are capable of altering their patterns of gene expression in response to extracellular cues

1) when/how a gene is transcribed

2) how an RNA transcript is spliced/processed

3) which mRNAs exit the nucleus

4) how quickly mRNA is degraded

5) which mRNAs are translated into protein by ribosomes

6) controlling the rate of proteolysis

Name the 6 ways gene expression can be regulated throughout the central dogma

transcript regulators

proteins that bind to regulatory DNA sequences and control gene transcription

regulatory DNA sequences

sequences that are used to switch the gene on or off; these are recognized by transcription regulators

transcription regulators

this interacts with the major groove of a DNA helix; the binding of this to a regulatory DNA sequence acts as the switch to control transcription

changes in the environment

transcriptional switches allow cells to respond to what?

operons

common in bacteria but rare in eukaryotes where genes are transcribed individually; this is a coordinately transcribed cluster of genes on a chromosome that are transcribed from a single promoter as one long mRNA molecule

tryptophan repressor

an allosteric protein that is a transcription regulator; when it binds to the operator, it blocks access of RNA polymerase to the promoter, preventing transcription of the operon and production of tryptophan-producing enzymes

lumen

ribosomes are actively synthesizing proteins that are delivered into the ER...